Association of DNA repair gene polymorphisms with colorectal cancer risk and treatment outcomes

MSH7 confers quantitative variation in pollen fertility and boosts grain yield in maize

Fertile pollen is critical for the survival, fitness, and dispersal of flowering plants, and directly contributes to crop productivity. Extensive mutational screening studies have been carried out to dissect the genetic regulatory network determining pollen fertility, but we still lack fundamental knowledge about whether and how pollen fertility is controlled in natural populations. We used a genome-wide association study (GWAS) to show that ZmGEN1A and ZmMSH7, two DNA repair-related genes, confer natural variation in maize pollen fertility. Mutants defective in these genes exhibited abnormalities in meiotic or post-meiotic DNA repair, leading to reduced pollen fertility. More importantly, ZmMSH7 showed evidence of selection during maize domestication, and its disruption resulted in a substantial increase in grain yield for both inbred and hybrid. Overall, our study describes the first systematic examination of natural genetic effects on pollen fertility in plants, providing valuable genetic resources for optimizing male fertility. In addition, we find that ZmMSH7 represents a candidate for improvement of grain yield.

The underlying mechanism of nuclear and mitochondrial DNA damages in triggering cancer incidences: Insights into proteomic and genomic sciences

The attempt of this review article is to determine the impact of nuclear and mitochondrial damages on the propagation of cancer incidences. This review has advanced our understanding to altered genes and their relevant cancerous proteins. The progressive raising effects of free reactive oxygen species ROS and toxicogenic compounds contributed to significant mutation in nuclear and mitochondrial DNA where the incidence of gastric cancer is found to be linked with down regulation of some relevant genes and mutation in some important cellular proteins such as AMP-18 and CA-11. Thereby, the resulting changes in gene mutations induced the apparition of newly polymorphisms eventually leading to unusual cellular expression to mutant proteins. Reduction of these apoptotic growth factors and nuclear damages is increasingly accepted by cell reactivation effect, enhanced cellular signaling and DNA repairs. Acetylation, glycation, pegylation and phosphorylation are among the molecular techniques used in DNA repair for rectifying mutation incidences. In addition, the molecular labeling based fluorescent materials are currently used along with the bioconjugating of signal molecules in targeting disease translocation site, particularly cancers and tumors. These strategies would help in determining relevant compounds capable in overcoming problems of down regulating genes responsible for repair mechanisms. These issues of course need interplay of both proteomic and genomic studies often in combination of molecular engineering to cible the exact expressed gene relevant to these cancerous proteins.

Update on Emerging Therapies for Advanced Colorectal Cancer

Colorectal cancer (CRC) is the third most common malignancy worldwide. It is projected to increase by 3.2 million new cases and account for 1.6 million deaths by 2040. Mortality is largely due to limited treatment options for patients who present with advanced disease. Thus, the development of effective and tolerable therapies is crucial. Chemotherapy has been the backbone of systemic treatment of advanced CRC, but utility has been limited because of invariable resistance to therapy, narrow mechanisms of action, and unfavorable toxicity profile. Tumors that are mismatch repair-deficient have demonstrated remarkable response to immune checkpoint inhibitor therapy. However, most CRC tumors are mismatch repair-proficient and represent an unmet medical need. Although ERBB2 amplification occurs only in a few cases, it is associated with left-sided tumors and a higher incidence of brain metastasis. Numerous combinations of HER2 inhibitors have demonstrated efficacy, and antibody-drug conjugates against HER2 represent innovative strategies in this area. The KRAS protein has been classically considered undruggable. Fortunately, new agents targeting KRAS G12C mutation represent a paradigm shift in the management of affected patients and could lead the advancement in drug development for the more common KRAS mutations. Furthermore, aberrant DNA damage response is present in 15%-20% of CRCs, and emerging innovative combinations with poly (ADP-ribose) polymerase (PARP) inhibitors could improve the current therapeutic landscape. Multiple novel biomarker-driven approaches in the management of patients with advanced CRC tumors are reviewed in this article.

Association of buccal micronucleus cytome assay (BMNCyt) biomarkers with inorganic element concentration and genetic polymorphisms in welders

Welding fumes are classified as carcinogenic to humans. The aim of the present study was to measure buccal micronucleus cytome assay biomarkers and to evaluate their association with inorganic elements and genetic polymorphisms (XRCC1, OGG1, XRCC3, GSTM1, and GSTT1) in welders (n = 98) and control individuals (n = 100). Higher levels of DNA damage and cell death were observed in the exposed group. Also, a significant correlation between the frequency of micronuclei and Na, Si, Cl, Ti, Cr, Zn and Mg concentrations. The formation of micronuclei, binucleated cells, cell death was associated with polymorphisms in repair pathways. The OGG1Ser326Cys and XRCC3 241Thr/Met genotypes were associated with cell death. Individuals with GSTM1 null genotype had a higher frequency of micronuclei. These results demonstrate that the deleterious effects of exposure to welding fumes are exacerbated by lifestyle habits, and genetic polymorphisms can influence DNA damage and cell death.

Canonical and uncanonical pathogenic germline variants in colorectal cancer patients by next-generation sequencing in a European referral center

BACKGROUND

Despite increasing use of next-generation sequencing (NGS), data concerning the gain in germline pathogenic variants (PVs) remain scanty, especially with respect to uncanonical ones. We aimed to verify the impact of different cancer predisposition genes (CPGs) on colorectal cancer (CRC) in patients referred for genetic evaluation.

MATERIALS AND METHODS

We enrolled for NGS, by Illumina TruSight Cancer panel comprising 94 CPGs, 190 consecutive subjects referred for microsatellite instability (MSI) CRC, polyposis, and/or family history.

RESULTS

Overall, 51 (26.8%) subjects carried 64 PVs; PVs coexisted in 4 (7.8%) carriers. PVs in mismatch repair (MMR) genes accounted for one-third of variant burden (31.3%). Four Lynch syndrome patients (20%) harbored additional PVs (HOXB13, CHEK2, BRCA1, NF1 plus BRIP1); such multiple PVs occurred only in subjects with PVs in mismatch syndrome genes (4/20 versus 0/31; P = 0.02). Five of 22 (22.7%) patients with MSI cancers but wild-type MMR genes harbored PVs in unconventional genes (FANCL, FANCA, ATM, PTCH1, BAP1). In 10/63 patients (15.9%) with microsatellite stable CRC, 6 had MUTYH PVs (2 being homozygous) and 4 exhibited uncanonical PVs (BRCA2, BRIP1, MC1R, ATM). In polyposis, we detected PVs in 13 (25.5%) cases: 5 (9.8%) in APC, 6 (11.8%) with biallelic PVs in MUTYH, and 2 (3.9%) in uncanonical genes (FANCM, XPC). In subjects tested for family history only, we detected two carriers (18.2%) with PVs (ATM, MUTYH).

CONCLUSION

Uncanonical variants may account for up to one-third of PVs, underlining the urgent need of consensus on clinical advice for incidental findings in cancer-predisposing genes not related to patient phenotype.

Polymorphisms of nucleotide excision repair genes associated with colorectal cancer risk: Meta-analysis and trial sequential analysis

Background: Reduced DNA repair capacity in nucleotide excision repair (NER) pathways owing to genetic variant may influence cancer susceptibility. According to published studies, variants of NER genes associations with colorectal cancer (CRC) risk were inconclusive. Thus, this meta-analysis aimed to explore the possible association. A trial sequence analysis (TSA) analysis was performed to control the risk of false positive or false negative.

Methods: PubMed, Web of Science, Embase, Cochrane Library, China National Knowledge Network (CNKI), Wanfang Database and Scientific and Technical Journal Database (VIP) were searched to identify relative studies until April 2022. The association was assessed by odds ratio (OR) in Allele, homozygous, heterozygous, dominant, recessive, and over-dominant models. In addition, Begg’s and Egger’s tests, sensitivity analysis, subgroup analysis and TSA analysis were performed.

Results: A total of 29 studies were eventually included in the meta-analysis, including 12,153 CRC patients and 14,168 controls. It showed that excision and repair cross complementary group 1 (ERCC1) rs11615 CC genotype decreased the risk of CRC, compared with TT genotype (CC vs. TT: OR = 0.816, 95% CI = 0.673–0.990, p = 0.039). For ERCC1 rs3212986, the significant impact was detected on increased the risk of CRC in the allele (OR = 1.267, 95% CI = 1.027–1.562, p = 0.027), homozygous (OR = 1.805, 95% CI = 1.276–2.553, p = 0.001), dominant (OR = 1.214, 95% CI = 1.012–1.455, p = 0.037) and recessive (OR = 1.714, 95% CI = 1.225–2.399, p = 0.002) models, especially in the Asian population. The results revealed the association of ERCC2 rs1799793 A allele with a higher risk of CRC (A vs. G: OR = 1.163, 95% CI = 1.021–1.325, p = 0.023). It also showed that ERCC5 rs17655 increased CRC risk in the allele (OR = 1.104, 95% CI = 1.039–1.173, p = 0.001), homozygous (OR = 1.164, 95% CI = 1.018–1.329, p = 0.026), heterozygous (OR = 1.271, 95% CI = 1.018–1.329, p < 0.001), dominant (OR = 1.241, 95% CI = 1.135–1.358, p < 0.001) and over-dominant (OR = 0.828, 95% CI = 0.762–0.900, p < 0.001) models, especially among Asians.

Conclusion: This meta-analysis based on current evidence suggests that the significant association was observed between ERCC1 rs11615, ERCC1 rs3212986, ERCC2 rs1799793, and ERCC5 rs17655 and CRC susceptibility. However, given the limited sample size and the influence of genetic background, studies of a larger scale and well-designed are required to confirm the results.

The Roles of EXO1 and RPA1 Polymorphisms in Prognosis of Lung Cancer Patients Treated with Platinum-Based Chemotherapy

Background. Lung cancer is one of the major causes of cancer-related mortality worldwide. DNA repair and damage response contribute to genomic instability that accompanies tumor progression. In this study, we focus on evaluating association between DNA repair polymorphisms of EXO1, RPA1, and prognosis in lung cancer patients whom received platinum-based chemotherapy. Methods. 593 lung cancer patients were recruited in this study. We performed genotyping of 19 single nucleotide polymorphisms (SNPs) by Sequenom MassARRAY. Cox regression analysis was used to assess overall survival (OS) and progression-free survival (PFS) among SNP genotypes. Results. Significant differences in PFS and OS were observed in RPA1 rs5030740, EXO1 rs1776148, and rs1047840. Results showed that patients with CC genotype in rs5030740 (recessive model: $P=0.034$ ) had a better PFS. Patients with AA or/and AG genotypes in rs1776148 (additive model: $P=0.004$ ; dominant model: $P=0.048$ ) and AA genotype in rs1047840 (recessive model: $P=0.023$ ) had longer OS. We also demonstrated differences in subgroup analysis between rs5030740, rs1776148, rs1047840, and prognosis. Conclusions. Our results indicated that EXO1 rs1776148, rs1047840, and RPA1 rs5030740 were significantly associated with prognosis of lung cancer. Rs1776148, rs1047840, and rs5030740 may act as prognosis markers in lung cancer patients with platinum-based chemotherapy.

DNA Repair Genes Are Associated with Subtype Classification, Prognosis, and Immune Infiltration in Uveal Melanoma

Uveal melanoma (UM) is the most common primary intraocular malignancy in adults. DNA repair genes play a vital role in cancer development. However, there has been very little research about DNA repair genes in UM. This study aimed to evaluate the importance of DNA repair genes and established a signature for predicting prognosis and immune features of UM. In this study, we mined TCGA database through bioinformatics analysis, and the intersect was taken between DNA repair genes and prognosis related genes and yielded 52 genes. We divided 80 UM patients into C1 and C2 subtypes. GSEA results indicated that abundant cancer-promoting functions and signaling pathways were activated in C2 subtype and the proportion of SNVs was higher in C2 than in C1 which suggested a worse prognosis. We built a six DNA repair genes model including ITPA, CETN2, CCNO, POLR2J, POLD1, and POLA1 by LASSO regression to predict prognosis of UM patients and utilized the median value of risk scores as the cutoff point to differentiate high risk and low risk group. The survival analyses and the receiver operating characteristic (ROC) curves in the validation group and entire data set confirmed the accuracy of this model. We also constructed a nomogram based on age and risk scores to evaluate the relationship between risk scores and clinical outcome. The calibration curve of the overall survival (OS) indicated that the performance of this model is steady and robust. Finally, the enrichment analysis showed that there were complex regulatory mechanisms in UM patients. The immune infiltration analysis indicated that the immune infiltration in C2 in the high risk group was different from that in the low risk group. Our findings indicated that the DNA repair genes may be related to UM prognosis and provide new insight into the underlying mechanisms.

Polymorphism rs2682818 participates in the progression of colorectal carcinoma via miR-618-TIMP1 regulatory axis

Colorectal carcinoma (CRC) has a high morbidity and mortality. Current studies have confirmed a variety of microRNA polymorphisms were associated with tumor susceptibility, however, the mechanisms are still unknown. In this study, we were aimed to clarify how polymorphism rs2682818 participated in the progression of CRC. First of all, the differential expression of miR-618 was assessed by quantitative real-time polymerase chain reaction in CRC patients with different genotypes of polymorphism rs2682818, including homozygous (TT) genotype, homozygous (GG) genotype and heterozygous (TG) genotype. Secondly, plasmids carried miR-168 precursor sequences harboring rs2682818 (SNP type) or without rs2682818 (wild type) were transfected into 293T cells to verify that polymorphism rs2682818 affected miR-618 expression. Thirdly, CCK-8 assay, flow cytometry assay, transwell assay and mouse xenograft assay were performed to measure the biological functions of miR-618 in CRC. Fourthly, the candidate target genes of miR-618 which were predicted by bioinformatics tools were verified by luciferase reporter assay. Finally, in order to explain the potential molecular mechanisms, western blotting was performed to demonstrate the differential expression and phosphorylation of pathway related proteins. The results showed that miR-618 was down-regulated in colon cancer, especially in CRC patients with rs2682818 GG homozygous genotype. Higher expression of mature miR-618 occurred in patients with TT homozygous genotype, and these patients usually had a longer survival time. Moreover, miR-618 mimic obviously impaired the growth and invasion ability of CRC cells, and miR-618 mimic also remarkably promoted CRC cell apoptosis. Our luciferase experiments confirmed that TIMP1 was a target of miR-618 in CRC cells. Knockdown of TIMP1 also significantly inhibited the malignant cytological features of CRC, including malignant growth and invasion as well as apoptosis resistance. In summary, polymorphism rs2682818 participated in the progression of CRC via affecting the expression of mature miR-618 in CRC cells, and miR-618 inhibited the progression of CRC via targeting TIMP1expression.

Association between NER pathway gene polymorphisms and neuroblastoma risk in an eastern Chinese population

Neuroblastoma is a common childhood malignancy. Nucleotide excision repair (NER) polymorphisms have been shown to influence cancer susceptibility by modifying DNA repair efficiency. To investigate the association of NER gene polymorphisms with neuroblastoma risk, we constructed a three-center case-control study. A total of 19 candidate single-nucleotide polymorphisms (SNPs) in NER genes were analyzed. Odds ratios (ORs) and 95% confidential intervals (CIs) were calculated to evaluate the associations. We identified five independent SNPs that were significantly associated with neuroblastoma risk, including XPA rs1800975 (dominant model: adjusted OR = 0.73, 95% CI = 0.55-0.98, p = 0.033), XPA rs3176752 (recessive model: adjusted OR = 2.78, 95% CI = 1.12-6.91, p = 0.028), XPD rs3810366 (dominant: adjusted OR = 1.44, 95% CI = 1.05-1.97, p = 0.022; recessive: adjusted OR = 1.58, 95% CI = 1.18-2.11, p = 0.002), XPD rs238406 (dominant: adjusted OR = 0.64, 95% CI = 0.48-0.84, p = 0.002; recessive: adjusted OR = 0.67, 95% CI = 0.48-0.94, p = 0.021), and XPG rs2094258 (recessive: adjusted OR = 1.44, 95% CI = 1.03-2.04, p = 0.036). Stratified analysis was carried out. Furthermore, these findings were strengthened by false-positive report probability (FPRP) analysis and expression quantitative trait loci (eQTL) analysis. In conclusion, our study indicates that five SNPs in NER genes are correlated with neuroblastoma susceptibility in the eastern Chinese population, providing novel insight into the genetic underpinnings of neuroblastoma. However, further large-scale studies are required to verify these findings.

Influence of KDR Genetic Variation on the Efficacy and Safety of Patients with Chemotherapy Refractory Metastatic CRC Who Received Apatinib Treatment

Background

The aim of the present study was to investigate the influence of kinase insert domain containing receptor (KDR) genetic variation on the efficacy of treatment and safety of patients with chemotherapy-refractory metastatic colorectal cancer (CRC) receiving apatinib.

Methods

A total of 108 patients with chemotherapy refractory metastatic CRC who were treated with apatinib participated in this study retrospectively. Efficacy of the patients' treatment was evaluated. Prognosis was carried out and safety profile was documented, respectively. Blood specimens and peripheral blood mononuclear cells (PBMC) of the patients were obtained for the analysis of genetic variation and KDR gene mRNA expression, respectively. The association between genotype status and clinical outcomes was presented.

Results

Objective response rate (ORR) and disease control rate (DCR) of the 108 patients with metastatic CRC receiving apatinib treatment were 5.6% and 69.4%, respectively. Survival analysis results exhibited that the median progression-free survival (PFS) and overall survival (OS) of the 108 patients with metastatic CRC was 3.6 months (95% confidence interval (CI): 3.03-4.17 months) and 8.9 months (95% CI: 7.57-10.23 months), respectively. Subsequently, the analysis of KDR genetic variation indicated that rs2071559 was of clinical significance. The minor allele frequency of rs2071559 was 0.22 and the genotype status corresponded with Hardy-Weinberg equilibrium (P=0.949). Prognosis analysis in a dominant inheritance manner through the combination of patients with TC and CC genotype showed that the median PFS of patients with TT genotype and TC/CC genotype was 4.1 and 3.0 months, respectively (P=0.012). Furthermore, the median OS of patients with the two genotypes was 10.5 and 6.1 months, respectively (P=0.007). Additionally, multivariate Cox regression analysis of OS showed that TC/CC genotype was an independent factor for OS (Hazard ratio (HR)=0.65, P=0.021). Interestingly, mRNA expression analysis suggested that the mRNA expression of KDR in PBMC differed significantly according to rs2071559 genotype status (P<0.001).

Conclusion

Apatinib demonstrated a potentially superior clinical outcome for patients with chemotherapy-refractory metastatic CRC. KDR polymorphism rs2071559 could be used as a potential biomarker for the prognosis evaluation of patients with CRC receiving apatinib therapy.